Isomerization between runs

From: Michail Lazaratos (
Date: Wed Aug 01 2018 - 04:56:01 CDT

Dear NAMD users,

i want to introduce an isomerization of a bond in my retinal protein system.

I already have a 65 ns trajectory. Is it possible to set somehow in my
input file the dihedral angle C1-C2-C3-C4 for example to a specific value
and slowly equilibrate, until i can be able to restart my simulation from
the latest checkpoint?

Also, would there be a conflict since the latest checkpoint for the
coordinates would have different positions for atoms manipulated?

Thank you in advance,

Michail Lazaratos

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